Export/Import Screen Layouts
You can copy the startup.blend file from your old blender config directory to the new one.

Example:
(on most linux distros) ~/.blender/2.69/config/startup.blend -> ~/.blender/config/startup.blend.
On Mac OS, it'd be in ~/Library/Application Support/Blender/&lt;version&gt;/config. Not sure about windows.

The only other things that seem to be there are user-installed add-ons (in scripts rather than config), bookmarks (config/bookmarks.txt) and recently opened files (recent-files.txt). You should be able to copy those without an issue.

For the startup blendfile, it's probably a good idea to save your settings after having started up, or to just continue doing it as you wrote in your question, to make sure that the blendfile is actually of the right version. Shouldn't make a big difference what with it still being a blendfile and the great reverse compatibility in blender, but you never know!